FMA Chain of Command
by dacharya64
Summary: When Musang and some of his officers go on a secret undercover mission to an Ishbalan base, things go terribly wrong and Mustang is captured. Back at west HQ, Archer Mustang's temporary replacement refuses to help Mustang to protect theirfragile treaty.
1. Chapter 1

This is a fan-fic I made a while back. It's based on Fullmetal Alchemist and Star Trek The Next Generation's Chain of Command Pts 1-2. Please comment, I would really appreciate knowing that people are reading this. Without further ado, so let it begin!

**Part 1**

Mustang: I, Lt. Hawkeye, and Major Armstrong have been reassigned.

Havoc: Hmmmm?

Mustang: Yes. It is a highly secret mission for the military…

(Long pause)

Falman: …And?

Mustang: I'm afraid that's all I can tell you.

Breda: (Snorts) C'mon, Colonel…

Fuery: Yeah. If you couldn't trust us, we wouldn't be here.

Mustang: (Annoyed) That's true, but-

The four: Pleeeeeease?

Mustang: NO! (Stands)

(Mustang moves to door, then turns)

Mustang: Oh, and, by the way; Frank Archer will be in temporary command while I'm gone. I expect you to treat him…._ properly._

(Mustang leaves)

(The four exchange glances)

Black Hayate: (Whimper)

Hawkeye: Colonel, I think we've been through this earthquake simulation enough, now.

Mustang: Yes, you're probably right. Perhaps we should repeat the falling ro-

Armstrong: I have a feeling that the Lt. means that we have trained enough for today.

Hawkeye: We have no idea what we'll be facing in there. We don't even have schematics of the area.

Armstrong: The best thing for us right now would be a good night's sleep.

Mustang: (Sigh) Very well.

Archer: I was looking forward to commanding this post… (Walks in)

(The four jump to attention)

Archer: I heard from Colonel Mustang that you were some of the finest officers in the military. I'd like to change the way some things are run around here.

The four: Yes, sir!

Archer: At ease. Now first, this office is useless. How do you expect to do things around here with only four people? I will have to talk to the Fuhrer immediately. Get this place cleaned up _now_. Work overtime if you have to. (Prepares to leave) Oh, and… (turns) Get that mutt out of the office. I don't want dog hair in here. (leaves)

The four: (Shocked)

Breda: He can't just have us change our whole setup!

Fuery: Yeah, and what about Black Hayate?

Havoc: I can always…

Others: (Scowl)

(Mustang's office. Different officers mill about with papers)

Fuery: We've got to tell the Colonel about this. Archer's completely changed the way everything works here, and is massing more troops around Central.

Falman: I'm sure the Colonel can do something if we tell him.

(Fuery, Breda and Falman stare pointedly at Havoc)

Havoc: (Annoyed) Fine, I'll talk with him…

(Mess hall)

Mustang: (Drowsily sips tea)

Havoc: (Approaches) Hey, Roy! I wanted to ask you about something…

Mustang: (Yawn) I haven't worked this hard since… oh, forget it. Yes, what is it, Havoc?

Havoc: (Considerate) No, it's nothing, really…

Mustang: (Snore)

Breda: Sir, I've been meaning to talk to you…

Archer: About the change in command. I've noticed some…. _complications…_

Breda: It's been a bit difficult adjusting…. (Mutters) _As if that's our fault…_

Archer: I don't have time to baby-sit the soldiers at Eastern Headquarters. There are new uprisings, and I intend to be ready for them. Oh, and… (pause) When you're on duty, wear you're uniform properly.

Breda: (annoyed) Yes, sir.

(Private military train)

(Mustang, Hawkeye and Armstrong sit in one compartment)

Hawkeye: So can you tell us what our mission is now, sir?

Mustang: Yes. I'm sorry I wasn't able to inform you earlier, but I couldn't risk a leak in information. Anyway, our mission is to infiltrate a high-security Ishballan base, where they are believed to be researching military applications for the Philosopher's Stone.

Armstrong and Hawkeye: (Gasp)

Mustang: Needless to say, if they obtain this technology it could lead to the death of thousands. We are to go in and find out if they really are developing a Philosopher's Stones. If they are, we destroy the research.

Hawkeye and Armstrong: Yes, sir!

(Cave-like entryway)

Mustang: We're in.

(Various scenes of climbing through cave-like underground. Cliffs, tunnels, that sort of thing. Sparse conversation)

(Soon they arrive at a door in the rock face)

Mustang: Here we are. There will probably be Ishballans in here, so be ready.

(Mustang flames down door and the three enter the room)

Armstrong: There's… no one here. No evidence of alchemic research…

Hawkeye: A trap! Get down!

(Sounds of bullets being shot. Ishballans emerge from the shadows)

(Mustang is separated from the others during the battle)

(Backup door begins to lower)

Armstrong: The door! (Runs to the door and manages to hold it up with obvious effort) Sirs! We have to retreat!

Hawkeye: Come on, Colonel! (Runs out through door)

Armstrong: (Grunt) I can't hold it much longer!

Mustang: (Starts to door)

(Gun shot)

Armstrong: Agh! (Collapses back and out of room)

(Door slams shut)

Ishballan: Get your hands up.

Mustang: (Puts hands up)

(Sound of approaching footsteps)

Hawkeye: We have to go.

Armstrong: The Colonel…

Hawkeye: There's no time. We have to inform the military of this.

(They move out)

(Mustang is roughly shoved into a large, dark room by two Ishballan guards. A figure stands toward the back of the room. The darkness makes him too hard to see.)

Mustang: (To self) Where am I…?

Shadowed Figure (SF): Colonel Roy Mustang, the Flame Alchemist. Was in the Ishbal Rebellion, where he assisted in the escape of Dr. Tim Marcoh. Now serves in the military's Eastern Headquarters. His favorite food is… (pause) Gracia's apple pies.

Mustang: (Scared, angry) Who are you? Why did you bring me here? (Twitch) You're voice… It sounds…

SF: I am to be your questioner. You will either give me the answers I need… or die.

SO ENDS PART 1


	2. Chapter 2

Part 2

Mustang: (Drugged) Uhhhh….

SF: Where are the files on Tim Marcoh's research hidden?

Mustang: I… I don't know…

SF: Increase the dosage.

Ishballan: But sir, that might kill him!

SF: _Why do they always say that? _Just do it.

(Mustang is injected)

SF: Let's try this again…

Mustang: I demand to have a representative of a neutral party here to witness these events. I have rights as a prisoner of war!

SF: We contacted your military. They say you weren't acting under orders. Therefore you are subject to Ishballan laws… Including that of break-in and sabotage of a scientific installation…

Mustang: (Glare)

(Eastern Headquarters)

Hawkeye: You can't just say that the military wasn't responsible for this! The Colonel is subject to the rights of a prisoner of war!

Archer: If the Ishballans find out about what we've done, there could be another war. We have to do anything we can to avoid that.

Hawkeye: Then we need to mount a rescue operation.

Archer: I'm afraid that's the Fuhrer's decision to make, not yours.

Mustang: (Sleep- and food-deprived) Ugh….

SF: (Walks in) Hello, Colonel.

Mustang: You… you can't keep me here…

SF: But I can. (Presses button)

(Four bright lights come on behind SF. This only serves to darken his appearance even more)

Mustang: (Winces and shields eyes)

SF: So, Colonel, tell me: How many lights do you see?

Mustang: (Grunts, then squints blearily at the lights) There are…. four… lights…..

SF: You are mistaken, Colonel. There are five. (Presses button and Mustang is electrocuted) You have always been mistaken. About everything.

Mustang: (Collapses on the ground with a grunt, then looks up) What do you know about me? Nothing!

SF: I know more than you could ever imagine.

(Several days later)

(Lights are on. SF stands with back to them)

SF: How many lights are there?

Mustang: You're mad.

SF: There is nothing insane about torture, _Roy_. It's quite simple. First degrade the body, then the mind, then the soul. It even follows the most basic laws of alchemy. Analyze, break down, and reconstruct. It makes perfect sense in every way.

(Meanwhile, Mustang is having some problems. He knew he should know SF, but couldn't identify him… this was maddening)

Mustang: (In an explosion of temper) Who… WHO ARE YOU!?!

SF: Haven't you already guessed? (Presses torture button)

Mustang: (Collapses on ground)

(Several more days pass with similar results. [NOTE: Show some cool torture stuff here!])

Mustang: (Laying on ground, tightly gripping a poll in one hand. Haggard, bleary-eyed and thin.) Ugh… (Stands up and moves toward desk in middle of room. Sees torture device on there, and grabs it, repeatedly smashing into the ground.)

SF: (Comes in) Even in you did manage to destroy it, I have more.

Mustang: (Collapses on the ground, his energy spent)

SF: Get up. You're free to go.

Mustang: Go…? Just like that?

SF: Yes. I've gotten all I can out of you… (pause) though I will enjoy interrogating your friend Hawkeye…

Mustang: … (thinking) I'll stay. I'll take her place.

SF: Of your own free will?

Mustang: Yes.

SF: Very well…

(Prolonged torture, no sleep or food and the frustration at not knowing who SF was had taken their toll on Mustang)

Mustang: Why… (gasp) am I… (gasp) here…?

SF: How many lights do you see?

Mustang: What is this really about?

SF: Well, Colonel?

Mustang: (Hears a voice in his head… _Come on, Roy, you're being stupid again…_) (Stands) AND WHO THE HELL ARE YOU!?!

(Fatigue and dizziness come over him, and he faints)

Mustang: (Opens eyes wearily)

SF: I'd like you to meet my daughter.

Mustang: (Felt twinge of recognition, but was far past caring) What kind of despicable creature would let their own child witness the atrocities going on here?

SF: But she's been hoping to see you. She knows you, after all.

Mustang: …?

SF: Come on in… _Eilcia_.

Mustang: …… (Processing)

Elicia: Daddy! (Runs up to SF)

SF: (Immediately adopts caring tones) Hello, Elicia! (nuzzle)

Elicia: (Giggle)

Mustang: (Barely, under breath) …Maes…

SF: (Steps into the light. You can see that it's Hughes) Yo, Roy!

Mustang: …… ([Do some cool Hughes flashbacks]) You… you can't be…

SF (Now Hughes): (Grins. Pointy teeth revealed)

Mustang: (Realizes the truth) You…

Hughes: Gracia is very kind, isn't she? She brought you an apple pie! (Holds up basket)

Mustang: (Stares)

Hughes: Something wrong, Roy?

Mustang: Hughes is dead…that means…you must be…_a homunculus!_

Hughes: (To Elicia) Go on back home, Elicia. (To Mustang) Looks like you found me out, Roy. My wife is simply the _best_, isn't she?

Mustang: (Angry stare)

(Door shuts behind Elicia)

Hughes: (Adopts a crueler tone)You'd better eat this pie while it's still warm. _It's the last one Gracia will ever be making…_

Mustang: You… you killed her!

Hughes: You can't afford to get distracted by every little lost cause… you're own words, remember?

Mustang: Grrr…

Hughes: (Turns to face Mustang) So, you wanted to know what this was really all about. Well, I'll tell you. I may not be your Maes Hughes, but I still have a right to exist. And I could never rest knowing that you were still here, my past life would never allow it. But I thought before I saw you go I'd first break you down into the crude, brute barbarian that all humans really are.

Mustang: (Who is starting to really hate the sound of Hughes's voice) Why you… _you MONSTER!_ (Lunges at Hughes, trying to harm him in any way possible and fueled by sheer hatred)

Hughes: (Deftly dodges blows) Well, what's wrong, Roy? (This serves to irritate Mustang even further)

Mustang: (Aims another poorly judged blow, the only goal in his mind to silence the voice that was causing his to go through this torment…)

(Hughes strikes Mustang, causing him to collapse on the ground and curl up in pain, gasping for breath.)

Hughes: (Looms over Mustang) Now look who's the monster. Look at you, the pathetic dregs of humanity. Pitiful and crude, trying to harm everything that you can't handle. And when you finally realize that you have no power, you don't care about others, about how many people die, as long as it spares you any more pain. There really isn't such a thing as honor or loyalty; it's just a front you hide behind, trying to ignore the truth. And then you die. Perhaps it is when death finally comes, when you realize the truth, the whole totality of how the world really works: that is when all humans show their fear. But I'm afraid your time is up, Roy, and-

(Suddenly the door bursts open, and military troops flood in)

Hawkeye: Get your hands up! NOW!

(Hughes quickly makes his escape, jumping out through a window before anyone could identify him)

Hawkeye: (Sees dark heap on the floor) Colonel! COLONEL! (Runs over) Somebody help me get him up!

(Mustang is carried, whimpering, from the scene)

(Hospital, five days later)

Hawkeye: I read your report… Sir, what happened in there?

Mustang: (Continues to stare out window, then speaks) I saw Hughes in there… I thought I would never see him again… But there he was, standing right next to me. And all I wanted to do was to see him dead, to silence his voice, to end the pain.

Hawkeye: (Looks down) Sir…

Mustang: I saw the truth in there. I no that no one would ever like to admit it, but he spoke the truth. Just for a second, I saw the world for what it truly was. What do you think would've happened to me if you hadn't come? I would've been broken and lost, not knowing or caring about anyone but myself. And that would be how I died.

Hawkeye: (Angrily looks up) Sir, if that was really true, what Hughes's homunculus was saying, then why did you hesitate in Ishbal? If all people cared about was self-preservation, then why do you stop before the last blow? If there really was no sense of honor or justice, why would you serve the military and have loyal officers ready to serve you to the end?

Mustang: (Looks up at Hawkeye as if waking up from a dream) …Huh?

Hawkeye: That homunculus was trying to twist your perception, getting you to see truth out of lies. We both know there were only four lights.

Mustang: (Smiles faintly, then looks back at the window) (After a long pause) Yes, I know. But somehow it doesn't make me feel any better. (Looks down) I don't know if I can live life like this any longer… (Looks up suddenly) Lt. Hawkeye, get a search team on the homunculus's trail immediately. I want him apprehended.

Hawkeye: Uhn… Yes, sir! (Salute) … (Adopts a more caring tone) Don't worry, sir… things will turn out alright.

Mustang: Let's just hope so. Things must go on. No matter what happens.


End file.
